Physical activity surveillance in the European Union: reliability and validity of the European Health Interview Survey-PhysicalActivity Questionnaire (EHIS-PAQ)

Background: The current study examined the reliability and validity of the European Health Interview Survey-Physical Activity Questionnaire (EHIS-PAQ), a novel questionnaire for the surveillance of physical activity (PA) during work, transportation, leisure time, sports, health-enhancing and muscle-strengthening activities over a typical week. Methods: Reliability was assessed by administering the 8-item questionnaire twice to a population-based sample of 123 participants aged 15-79 years at a 30-day interval. Concurrent (inter-method) validity was examined in 140 participants by comparisons with self-report (International Physical Activity Questionnaire-Long Form (IPAQ-LF), 7-day Physical Activity Record (PAR), and objective criterion measures (GT3X+accelerometer, physical work capacity at 75 % (PWC75%) from submaximal cycle ergometer test, hand grip strength). Results: The EHIS-PAQ showed acceptable reliability, with a median intraclass correlation coefficient across PA domains of 0.55 (range 0.43-0.73). Compared to the GT3X+ (counts/minutes/day), the EHIS-PAQ underestimated moderate-to-vigorous PA (median difference - 11.7, p-value = 0.054). Spearman correlation coefficients (.) for validity were moderate-to-strong (rho's > 0.41) for work-related PA (IPAQ = 0.64, GT3X + = 0.43, grip strength = 0.48), transportation-related PA (IPAQ = 0.62, GT3X + = 0.43), walking (IPAQ = 0.58), and health-enhancing PA (IPAQ = 0. 58, PAR = 0.64, GT3X + = 0.44, PWC75% = 0.48), and fair-to-poor (rho's < 0.41) for moderate-to-vigorous aerobic recreational and muscle-strengthening PA. Conclusions: The EHIS-PAQ showed good evidence for reliability and validity for the measurement of PA levels at work, during transportation and health-enhancing PA

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruse

PhenoApp: A mobile tool for plant phenotyping to record field and greenhouse observations [version 2; peer review: 2 approved]

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data

The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU's zero pollution ambition

The chemical industry is the leading sector in the EU in terms of added value. However, contaminants pose a major threat and significant costs to the environment and human health. While EU legislation and international conventions aim to reduce this threat, regulators struggle to assess and manage chemical risks, given the vast number of substances involved and the lack of data on exposure and hazards. The European Green Deal sets a 'zero pollution ambition for a toxic free environment' by 2050 and the EU Chemicals Strategy calls for increased monitoring of chemicals in the environment. Monitoring of contaminants in biota can, inter alia: provide regulators with early warning of bioaccumulation problems with chemicals of emerging concern; trigger risk assessment of persistent, bioaccumulative and toxic substances; enable risk assessment of chemical mixtures in biota; enable risk assessment of mixtures; and enable assessment of the effectiveness of risk management measures and of chemicals regulations overall. A number of these purposes are to be addressed under the recently launched European Partnership for Risk Assessment of Chemicals (PARC). Apex predators are of particular value to biomonitoring. Securing sufficient data at European scale implies large-scale, long-term monitoring and a steady supply of large numbers of fresh apex predator tissue samples from across Europe. Natural science collections are very well-placed to supply these. Pan-European monitoring requires effective coordination among field organisations, collections and analytical laboratories for the flow of required specimens, processing and storage of specimens and tissue samples, contaminant analyses delivering pan-European data sets, and provision of specimen and population contextual data. Collections are well-placed to coordinate this. The COST Action European Raptor Biomonitoring Facility provides a well-developed model showing how this can work, integrating a European Raptor Biomonitoring Scheme, Specimen Bank and Sampling Programme. Simultaneously, the EU-funded LIFE APEX has demonstrated a range of regulatory applications using cutting-edge analytical techniques. PARC plans to make best use of such sampling and biomonitoring programmes. Collections are poised to play a critical role in supporting PARC objectives and thereby contribute to delivery of the EU's zero-pollution ambition.Non peer reviewe

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses

Development of humoral immune responses following DNA immunization.

<p>At the indicated time points, Gag-specific serum antibody titers were analyzed using an ELISA. Data are shown as geometric mean of six animals per group (#, p<0.05 compared with C and D; non-parametric ANOVA (Kruskal-Wallis) followed by a Dunns Post test).</p

Development of proliferative CD4⁺ and CD8⁺ T-cell responses following DNA immunization.

<p>Before and at the indicated time points following immunization, CFSE-labeled PBMCs were incubated with AT-2 SIV or microvesicles. On day 7, T-cell proliferation was assessed as the percentage of CFSE^low CD4⁺ (gating on live CD3⁺CD8⁻, A) and CD8⁺ (gating on live CD3⁺CD8⁺, B) T cells. Data obtained with microvesicles were subtracted, and means and standard error of the means (SEM) are shown (#, p<0.05 compared with C and D, †, p<0.05 compared with A; one-way ANOVA followed by Bonferroni Post test; *, p<0.05 for differences to baseline; two-way ANOVA).</p

Principle of targeting of antigens encoded by DNA vaccines to DCs.

<p>The coding region of variable heavy (V_H) and light (V_L) chains of antibodies to uptake receptors of DCs are fused in frame to the open reading frame of the antigen. After delivery of the DNA vaccine, transduced cells of the immunized individual produce and secret a single chain antibody to the uptake receptor coupled to the antigen. Binding of the single chain to the uptake receptors should increase uptake and presentation of the antigen by the DCs.</p

Expression and characterization of the antigen and verification of binding to rhesus macaque DCs.

<p>293 T cells were transiently transfected with grading doses (from 3 to 0,003 µg) of scISO-p27 or scDEC-p27 expressing plasmids (pV-scISO-p27 or pV-scDEC-p27). Additionally, 293 T cells were transfected with 3 µg of a GFP-expressing plasmid as negative control. Supernatants were harvested 48 h after transfection and secreted fusion proteins were detected by Western Blot analysis to confirm comparable expression levels (A). Monocyte-derived rhesus macaque DCs were incubated with supernatants of transfected 293 T cells, and bound fusion proteins were visualized by using an Alexa647-labeled α-OLLAS antibody. Subsequent FACS-analyses are shown for scDEC-p27 (filled grey histogram) and scISO-p27 (open black histogram) for immature and mature DCs (B).</p

Analysis of cytokine secretion by PBMCs following SIV-restimulation.

<p>At the indicated time points, PBMC were incubated with AT2-inactivated SIV, microvesicles, or SEB as control. Culture supernatants were harvested after 48 h and concentrations of IFN-γ were determined by ELISA. Data obtained with microvesicles were subtracted, and means and SEM are shown (#, p<0.05 compared with C and D, †, p<0.05 compared with A; one-way ANOVA followed by Bonferroni Post test; *, p<0.05 for differences to baseline; two-way ANOVA). Substantial concentrations of IL-4, IL-10, or IL-17 were not detected in supernatants of SIV-stimulated cells derived from either group (data not shown).</p